Universality in protein residue networks

Ernesto Estrada, New Professor's Fund - University of Strathclyde (Funder)

Research output: Contribution to journalArticle

43 Citations (Scopus)

Abstract

Residue networks representing 595 nonhomologous proteins are studied. These networks exhibit universal topological characteristics as they belong to the topological class of modular networks formed by several highly interconnected clusters separated by topological cavities. There are some networks which tend to deviate from this universality. These networks represent small-size proteins having less than 200 residues. We explain such differences in terms of the domain structure of these proteins. On the other hand, we find that the topological cavities characterizing proteins residue networks match very well with protein binding sites. We then investigate the effect of the cutoff value used in building the residue network. For small cutoff values, less than 5Å, the cavities found are very large corresponding almost to the whole protein surface. On the contrary, for large cutoff value, more than 10.0 Å, only very large cavities are detected and the networks look very homogeneous. These findings are useful for practical purposes as well as for identifying "protein-like" complex networks. Finally, we show that the main topological class of residue networks is not reproduced by random networks growing according to Erdös-Rényi model or the preferential attachment method of Barabási-Albert. However, the Watts-Strogatz (WS) model reproduces very well the topological class as well as other topological properties of residue network. We propose here a more biologically appealing modification of the WS model to describe residue networks.
LanguageEnglish
Pages890-900
Number of pages11
JournalBiophysical Journal
Volume98
Issue number5
DOIs
Publication statusPublished - 3 Mar 2010

Fingerprint

Proteins
Membrane Proteins
Protein Domains

Keywords

  • protein residue networks
  • modular networks
  • random networks

Cite this

Estrada, E., & New Professor's Fund - University of Strathclyde (Funder) (2010). Universality in protein residue networks. Biophysical Journal, 98(5), 890-900. https://doi.org/10.1016/j.bpj.2009.11.017
Estrada, Ernesto ; New Professor's Fund - University of Strathclyde (Funder). / Universality in protein residue networks. In: Biophysical Journal. 2010 ; Vol. 98, No. 5. pp. 890-900.
@article{7f16d0e3dcd5476ca0bafab9925bfd70,
title = "Universality in protein residue networks",
abstract = "Residue networks representing 595 nonhomologous proteins are studied. These networks exhibit universal topological characteristics as they belong to the topological class of modular networks formed by several highly interconnected clusters separated by topological cavities. There are some networks which tend to deviate from this universality. These networks represent small-size proteins having less than 200 residues. We explain such differences in terms of the domain structure of these proteins. On the other hand, we find that the topological cavities characterizing proteins residue networks match very well with protein binding sites. We then investigate the effect of the cutoff value used in building the residue network. For small cutoff values, less than 5{\AA}, the cavities found are very large corresponding almost to the whole protein surface. On the contrary, for large cutoff value, more than 10.0 {\AA}, only very large cavities are detected and the networks look very homogeneous. These findings are useful for practical purposes as well as for identifying {"}protein-like{"} complex networks. Finally, we show that the main topological class of residue networks is not reproduced by random networks growing according to Erd{\"o}s-R{\'e}nyi model or the preferential attachment method of Barab{\'a}si-Albert. However, the Watts-Strogatz (WS) model reproduces very well the topological class as well as other topological properties of residue network. We propose here a more biologically appealing modification of the WS model to describe residue networks.",
keywords = "protein residue networks, modular networks, random networks",
author = "Ernesto Estrada and {New Professor's Fund - University of Strathclyde (Funder)}",
year = "2010",
month = "3",
day = "3",
doi = "10.1016/j.bpj.2009.11.017",
language = "English",
volume = "98",
pages = "890--900",
journal = "Biophysical Journal",
issn = "0006-3495",
number = "5",

}

Estrada, E & New Professor's Fund - University of Strathclyde (Funder) 2010, 'Universality in protein residue networks' Biophysical Journal, vol. 98, no. 5, pp. 890-900. https://doi.org/10.1016/j.bpj.2009.11.017

Universality in protein residue networks. / Estrada, Ernesto; New Professor's Fund - University of Strathclyde (Funder).

In: Biophysical Journal, Vol. 98, No. 5, 03.03.2010, p. 890-900.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Universality in protein residue networks

AU - Estrada, Ernesto

AU - New Professor's Fund - University of Strathclyde (Funder)

PY - 2010/3/3

Y1 - 2010/3/3

N2 - Residue networks representing 595 nonhomologous proteins are studied. These networks exhibit universal topological characteristics as they belong to the topological class of modular networks formed by several highly interconnected clusters separated by topological cavities. There are some networks which tend to deviate from this universality. These networks represent small-size proteins having less than 200 residues. We explain such differences in terms of the domain structure of these proteins. On the other hand, we find that the topological cavities characterizing proteins residue networks match very well with protein binding sites. We then investigate the effect of the cutoff value used in building the residue network. For small cutoff values, less than 5Å, the cavities found are very large corresponding almost to the whole protein surface. On the contrary, for large cutoff value, more than 10.0 Å, only very large cavities are detected and the networks look very homogeneous. These findings are useful for practical purposes as well as for identifying "protein-like" complex networks. Finally, we show that the main topological class of residue networks is not reproduced by random networks growing according to Erdös-Rényi model or the preferential attachment method of Barabási-Albert. However, the Watts-Strogatz (WS) model reproduces very well the topological class as well as other topological properties of residue network. We propose here a more biologically appealing modification of the WS model to describe residue networks.

AB - Residue networks representing 595 nonhomologous proteins are studied. These networks exhibit universal topological characteristics as they belong to the topological class of modular networks formed by several highly interconnected clusters separated by topological cavities. There are some networks which tend to deviate from this universality. These networks represent small-size proteins having less than 200 residues. We explain such differences in terms of the domain structure of these proteins. On the other hand, we find that the topological cavities characterizing proteins residue networks match very well with protein binding sites. We then investigate the effect of the cutoff value used in building the residue network. For small cutoff values, less than 5Å, the cavities found are very large corresponding almost to the whole protein surface. On the contrary, for large cutoff value, more than 10.0 Å, only very large cavities are detected and the networks look very homogeneous. These findings are useful for practical purposes as well as for identifying "protein-like" complex networks. Finally, we show that the main topological class of residue networks is not reproduced by random networks growing according to Erdös-Rényi model or the preferential attachment method of Barabási-Albert. However, the Watts-Strogatz (WS) model reproduces very well the topological class as well as other topological properties of residue network. We propose here a more biologically appealing modification of the WS model to describe residue networks.

KW - protein residue networks

KW - modular networks

KW - random networks

UR - http://www.scopus.com/inward/record.url?scp=77749318502&partnerID=8YFLogxK

UR - http://www.cell.com/biophysj/

U2 - 10.1016/j.bpj.2009.11.017

DO - 10.1016/j.bpj.2009.11.017

M3 - Article

VL - 98

SP - 890

EP - 900

JO - Biophysical Journal

T2 - Biophysical Journal

JF - Biophysical Journal

SN - 0006-3495

IS - 5

ER -

Estrada E, New Professor's Fund - University of Strathclyde (Funder). Universality in protein residue networks. Biophysical Journal. 2010 Mar 3;98(5):890-900. https://doi.org/10.1016/j.bpj.2009.11.017